I agree with Sam... the intent of the warning is to get you to look over the geometry to make sure nothing odd happened. Another problem I've had is that sometimes one of the faces will be copied, but the edges are still connected to the original volume, so you don't notice it until you try to mesh and you get weird things going on. The easy way to check is to turn off the volume, and if there are any faces remaining, then that's what happened. But like Sam said, it only happens sometimes, and typically there's nothing wrong.